MolNFT v1 · #92613 · protein

Structure of fmta-like protein

4GDN · Protein flp: “Structure of fmta-like protein”. X-ray diffraction, 17 pockets (best druggability 0.68). MolNFT v1 #92613 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4GDN
Type: protein
Length: 1,334 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein flp
EC: 3.5.-.-
UniProt: Q7A3Q5
Pockets: 17 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 33% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protein flp (EC 3.5.-.-)	protein	336	34% helix, 23% strand	Q7A3Q5
C	Protein flp (EC 3.5.-.-)	protein	329	33% helix, 24% strand	Q7A3Q5
D	Protein flp (EC 3.5.-.-)	protein	333	32% helix, 23% strand	Q7A3Q5

Ligands and binding sites

PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	81	0.68	0.93	21	empty
2	421	0.67	0.79	38	empty
3	456	0.65	0.78	56	empty
4	418	0.60	0.76	53	empty
5	451	0.58	0.74	57	empty

Interfaces

5 interfaces between chains.

A–B · 809 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 426 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 414 Å² buried · 1 hydrogen bond · protein-protein
A–D · 208 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 183 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4GDN · Structure of FmtA-like protein · the same entry in another collection · chain D against D, TM-score 1.00
Q7A3Q5 · AlphaFold monomer V2.0 prediction for protein flp (Q7A3Q5) · a predicted model of the same protein · chain C against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q7A3Q5
Elsewhere: RCSB PDB 4GDN · PDBe 4GDN · UniProt Q7A3Q5

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